Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_029000246.1 H537_RS0126340 D-glycerate dehydrogenase
Query= curated2:Q9YAW4 (335 letters) >NCBI__GCF_000430725.1:WP_029000246.1 Length = 323 Score = 202 bits (515), Expect = 7e-57 Identities = 128/320 (40%), Positives = 178/320 (55%), Gaps = 6/320 (1%) Query: 1 MKRPRVFVTREVFPEALELLSKYYDVEVWDKYQPPPYETLLSKAREADALYTLLTDRIDC 60 M R V V R + P+ L +++ +DV V D + + L +A L + +D Sbjct: 1 MNRKNVVVFRALPPDLLARITERHDVVVADPRRTEERQRFLDALPQAQGLIGS-SFALDA 59 Query: 61 DLLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAEFTWALILAAARRV 120 L +AP L +++ ++VG DN ++ R GI + NTPGVLTE TA+ +ALIL A+RR+ Sbjct: 60 QTLDRAPALEVISSISVGVDNYELPYLERRGITLCNTPGVLTETTADTLFALILCASRRL 119 Query: 121 VEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVAE-IGKAFGMRIIY 179 VE + VR G W R G + G ++ GKTLGILG GRIG +A FGM ++Y Sbjct: 120 VELSNLVREGRWTR-NIGED---LFGWDVHGKTLGILGFGRIGQALARRAALGFGMPVLY 175 Query: 180 HSRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAILVN 239 H R E ++++L+ +DI+++ LPL++ TR L+G E LMK AI VN Sbjct: 176 HDPFEVRVPELSGLVTRLPMDEVLQRADIVALTLPLSEATRGLMGAREFALMKSGAIFVN 235 Query: 240 TGRGAIVDTGALVKALREGWIAAAALDVFEEEPLNPNHPLTAFKNVVLAPHAASATRETR 299 RG +V AL++AL G + AAALDVF EPL PL V PH SAT ETR Sbjct: 236 GARGGLVQEDALLQALDNGPLRAAALDVFATEPLPQASPLRTHPRVTPLPHIGSATHETR 295 Query: 300 LRMAMMAAENLVAFAQGKVP 319 MA +A ENL+A G+ P Sbjct: 296 RAMAELATENLLAVLDGEPP 315 Lambda K H 0.322 0.136 0.406 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 253 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 335 Length of database: 323 Length adjustment: 28 Effective length of query: 307 Effective length of database: 295 Effective search space: 90565 Effective search space used: 90565 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory